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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct...

Basic information

species Vitis vinifera
transcript Vv06s0004g08210.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g60330.1 (Oryza sativa), 5'ss of exon 1
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct----
|  |||||||| ||| | ||||| || ||||||||||||||||||||||| ||||| ||||||||| || ||  ||| ||| |  | |   | ||||||||||||||||||       | ||||| ||  | | || | |   |   ||       | ||    ||    |  ||||         ||| | || |||      
CAGAATGTTGTCCCATTGCGTGCCTACTATTACTCCAAGGATGAGAAGCTACTGGTGTATGACTATATCCCATCTGGTAGCCTTGCTGTTGTTTTGCATGgtatgcatttttc---ctcttttacatttgaac-tatttacctatctatttctgaaatctgaacatttagactatggagggctcctgcttttattcttagatga

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os05g40200.1 (Oryza sativa), 5'ss of exon 2
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct--
| ||||| ||| | | | |||||||| |||||||||||||| ||||||||  |||| ||||||||| |  ||  ||| ||| | |  ||    |||||||||||||  || || |    | |||     |  |||   | | ||   | |         | || |   | |   |  || ||| |       | |  |    
CAAAATGCTGTTCAATTGCGTGCTTACTATTACTCCAAGGACGAGAAGCTTTTGGTGTATGACTATATGACACCTGGTAGCCTTTGTGCTGCTTTGCATGgtatgctattacttcaaatcattaagccttt-cattgcctgacaga-acctgttttgtttgtgcaaagtgaatttattagctggttttaactacatataggc

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G045449_T01 (Zea mays), 5'ss of exon 1
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagc-atcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct
|  ||  |||| ||| | |||||||| || ||||||||||||||||||||| |||| |||||||||||| ||   || ||| | |  ||    ||||||||||||     |  | |||   | | ||    | || ||    ||     | |   |  |   ||   |||    ||  ||  |   |    | |  ||  |
CAGAACATTGTCCCATTGCGTGCTTACTACTACTCCAAGGATGAGAAGCTCTTGGTGTATGACTATGTCCCACTAGGTAGCCTTTGTGCTGCTTTGCATGgtatgtcccattcatttcaaataatctgtctgaatcattttacattttgttacctgtcatattgttagattgaaatt-tagttttcaaaattgaagctatt

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AC214817.3_FGT004 (Zea mays), 5'ss of exon 1
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataat----cagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct
|  ||   ||  ||| | |||||||| || ||||||||||||||||||||| |||| |||||||||||| ||   || ||| | |  ||    |||||||||||||    || | |||   | | ||    | || ||    || |     | |      |    |  ||    ||   | |   ||| |  || |    ||  
CAGAACACTGCCCCATTGCGTGCTTACTACTACTCCAAGGATGAGAAGCTCTTGGTGTATGACTATGTCCCACTAGGTAGCCTTTGTGCTGCTTTGCATGgtatgc--cctccatttcaaataatctgtctgaatcattttacattttgttacctgtcatattgttagattgaaatttagtt--ttgaaaattgaagctatttg

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G032384_T01 (Zea mays), 5'ss of exon 2
-------CCAAATGTTGTGCCACTCCGTGCTTATTATTAC-TCCAAGGATGAGAAGCTCCTGGTTTATGACTATG--TCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatg-atcatcatggtaactgatagctgtaatacttct
       |   | | ||   ||  | ||| |  | |  |  |  || || | |  |            || | ||     ||| ||| |||| || ||||  |||   | | ||        |   |||| || | | ||  | || |    |||| || | |||   ||||   || || |  |||    |   |||             
AGCTGTTCTGGAGGATGGAACAA-CAGTGGTGGTCAAGAGATTGAAAGAAGTGGTGGCGGGAAAGAGGGAATTTGAACAGCAGATGG-AGCTAATTGGCAAGgtttgctagcatcagaacattg--tcccattgcgtgcttac-tactactccaaggatgagaag---ctcttggtgtatgactatgtc--ccactag-------------

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G083188_T01 (Zea mays), 5'ss of exon 2
------CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagc-atcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct
      |  ||   ||| ||| | |||||||| || ||||||||||||||||||||| |||| ||||      || ||   || ||| | |  ||    ||||||||||||     |  | |||   | | ||    | || ||    ||     | |   |  |   ||   |||    ||  ||  |   |    | |  ||  |
CAGCATCAGAACACTGTCCCATTGCGTGCTTACTACTACTCCAAGGATGAGAAGCTCTTGGTGTATG------TCCCACTAGGTAGCCTTTGTGCTGCTTTGCATGgtatgtccccttcatttcaaataatctgtctgaatcattttacattttgttacctgtcatattgttagattgaaatt-tagttttcaaaattgaagctatt

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G465771_T01 (Zea mays), 5'ss of exon 1
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgc--att-ttctactt-ccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatc-atcatggtaactgatagctgtaatacttct
| ||||||  | ||| | || ||||||||||||||||||||||||||  |  |||| | ||| |||||| ||  ||| ||| |  | |   | |||||||||| ||  ||| || | | |     ||   || || |      | |    | |||| |   |  ||  |  ||  |  | ||| ||   |   || | ||     
CAAAATGTCATTCCATTGCGGGCTTATTATTACTCCAAGGATGAGAAATTGTTGGTGTTTGATTATGTCCCATCTGGTAGCCTTGCTGTTGTTTTGCATGgtaggctcattattttgcctatttcttgatttttaactgttcaacttgttcctcaatattgaagctagaaaatagactaaggtcacatttgaatgcacta-----

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA02G40340.1 (Glycine max), 5'ss of exon 2
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct----
|||||||||||||| || |||||||||||||| || ||||| ||||||||| |||||||||||||  || || ||||||   ||||  | || ||||||||||||||||| ||  ||| | |    ||  ||   | ||  | || | |      |   ||||  |  ||   ||   |  | |||  | | || | |      
CCAAATGTTGTGCCCCTTCGTGCTTATTATTATTCTAAGGACGAGAAGCTCTTGGTTTATGACTACATCCCAAGTGGCAATCTATCTACCCTCTTGCATGgtatgcattt-ctgtttctcctag--tttcagttaagtctttaaaacttgtttttgttttctgt-tattctatatttgagattatacatattatgcatgagctt

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA14G38630.1 (Glycine max), 5'ss of exon 1
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagc-atcaaaaggaactctgaatg-atcatcatggtaactgatagctgtaatacttct
|||||||||||||| || |||||||||||||| || ||||| ||||||||| |||||||||||||  || || ||||||   ||||  | || |||||||||||||||||  |  || |   ||  |||    |        |||    |   |     || | | |   |  |   | | | | ||   |    |  |  |
CCAAATGTTGTGCCCCTTCGTGCTTATTATTATTCTAAGGACGAGAAGCTCTTGGTTTATGACTACATCCCAAGTGGCAATCTATCTACCCTCTTGCATGgtatgcatttctt--tttctcctagtttcagttaaggctttacaacttgttttagttgtctgttattctgtatttgagattattcatgttttgcgtgatctt

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA11G31440.1 (Glycine max), 5'ss of exon 2
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt--tctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct
 |||||||||||||||| || ||||||||||| || || ||||| |||||  |||| |||||||||||| ||||||||| | ||    |||| |||||||||||||||||  | | |||   ||    || |    |||  | ||||   || |||   |  ||   |     | ||      ||   | |    || ||  
ACAAATGTTGTGCCACTTCGCGCTTATTATTATTCAAAAGATGAAAAGCTTTTGGTATATGACTATGTCCCAGGTGGCAACCTACACACACTCTTGCATGgtatgcatttattttccttagtttctgattttctgctaaatattcaaaattctaaaattaaacttgttttcttttatcccttttgcgggtttgtttaatt--

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA18G05740.1 (Glycine max), 5'ss of exon 2
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt--tctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagct-gtaatacttct
 ||||||||||||| || |||||||||||||| || || ||||| || ||  |||| |||||||||||| | ||||||| | ||    |||| ||||| |||||||||||  | |||||   ||    || |    |||  | ||||   || |||   |  ||   |     | ||      ||   ||| ||  || |   
ACAAATGTTGTGCCGCTTCGTGCTTATTATTATTCAAAAGATGAAAAACTTTTGGTATATGACTATGTCCCTGGTGGCAACCTACACACACTCTTGCACGgtatgcatttcttttacttagtttctgattttctgttaaatattcaaaattctaaaattaaacttgttttcttttatcccttgtgtgggcttgttttatt---

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT5G58300.1 (Arabidopsis thaliana), 5'ss of exon 2
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct
|| | ||| || || |||||||| ||||| ||||||||||||||||||||| |||||| ||| |||  | | | ||| | ||||||  ||||  | || |||  |  |||||| | | ||||    |  | |  ||   | | |  | ||    |      | |  ||  ||| || |  | ||| ||  | | |     
CCTAGTGTGGTTCCCCTCCGTGCATATTACTACTCCAAGGATGAGAAGCTCATGGTTTGTGATTATTACCCTGCTGGTAACTTATCATCACTACTCCACGgttag--ttttcttcctaccttcgtttaatggttta--tattta--cctcgttggtgtacttaa--gaatatcttgatttc-gat-gccatgacag----

upper sequence: Vv06s0004g08210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S3_381V6.1 (Physcomitrella patens), 5'ss of exon 4
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct-----------------------------------
| |||| | ||||| || || |||||||| | |||||||||||||||||||||||||| ||||||  |  |    |||||| | ||  | ||  | ||  |||  ||| ||       |||    | |    || |  |   |   | |  ||    |   |  ||| ||||  ||  |  | ||  || | ||    |                                    
CGAAATTTGGTGCCCCTTCGCGCTTATTACTTCTCCAAGGATGAGAAGCTCCTGGTTTCTGACTACCTGCCGATGGGCAGCCTCTCTTCCCTTCTTCACAgtaaacatcttgccagatcctccgtcctgatacaaatcctcgctttcgttgaacttcatcttttatgttcatggtgtgatgtaatcactttgattagacattgaatggcactccattctgtttcttgcttgtcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110702068|gb|EE080360.1|EE080360
EST:     CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATG                         GAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
genomic: CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt ... ttgcatgcagGAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
EST: gi|110371150|gb|EC934945.1|EC934945
EST:     CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATG                         GAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
genomic: CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt ... ttgcatgcagGAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
EST: gi|77580433|gb|DV219099.1|DV219099
EST:     CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATG                         GAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
genomic: CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt ... ttgcatgcagGAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
EST: gi|110384129|gb|EC948546.1|EC948546
EST:     CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATG                         GAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
genomic: CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt ... ttgcatgcagGAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
EST: gi|71864668|gb|DT013723.1|DT013723
EST:     CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATG                         GAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
genomic: CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt ... ttgcatgcagGAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
EST: gi|110699173|gb|EE075941.1|EE075941
EST:     CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATG                         GAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
genomic: CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt ... ttgcatgcagGAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
EST: gi|77580532|gb|DV219161.1|DV219161
EST:     CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATG                         GAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
genomic: CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt ... ttgcatgcagGAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
EST: gi|110713572|gb|EE089609.1|EE089609
EST:     CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATG                         GAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA
genomic: CCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattt ... ttgcatgcagGAAACAGGCCTACTGGACGATCTCCACTGGACTGGAATGCAAGAGTGAAGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAATGTTGTGCCACTCCGTGCTTATTATTACTCCAAGGATGAGAAGCTCCTGGTTTATGACTATGTCTCAGGTGGCAGCTTATCGGCACTGTTGCATGgtatgcattttctacttccctttaccttctagcataatcagtcaagcatcaaaaggaactctgaatgatcatcatggtaactgatagctgtaatacttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaac